Evolutionary lottery of skull and beak morphology
gif provided by the awesome Jen Bright @MorphobeakGeek!
In this exercise we will use a github repo to collaboratively collate and simulate evolutionary trajectories for each participants’ species body size using a simple brownian motion evolutionary model. This assumes evolutionary steps to progress comletely at random. You could say:
it’s a bit of lottery!
Each participant has created and contributed a file specifying the parameters required to simulate and plot their species evolutionary trajectory. We’ve collect all participants’ files in the master repo. Next we need to simulate species trajectories plot them up.
Participants will then get to see the skull and beak shape corresponding to their species relative body size!
setup
First we load the required packages and create some objects to compile data on trait evolution for each species.
require(dplyr)
require(ggplot2)
require(plotly)
set.seed(1)
t <- 0:100 # generate time vector
dt <- NULL # generate object to compile time-series data
cols <- NULL # generate object to compile trendline coloursSimulate trait evolution, iterate over all species files in
params/ folder
We’ll use the parameters supplied in your scripts to generate brownian trait evolution trendline for each species.
spp.files <- dir("params/")[dir("params/") != "params_tmpl.R"]
for(spp in spp.files){
# source parameters for each species
source(file.path("params", spp))
# generate trait evolution time-series and compile plotting data
dt <- rbind(dt, data.frame(t,
trait = c(0, rnorm(n = length(t) - 1, sd = sqrt(sig2)) %>% cumsum()),
species = species.name))
cols <- c(cols, color)
}Plot trait evolution timeseries
Use the data generated to plot all species.
p <- ggplot(data = dt, aes(x = t, y = trait, group = species, colour = species)) +
geom_line() +
scale_colour_manual(values = cols)
ggplotly(p)Skulls! find the skull associated with your species:
Skulls are organised from largest to smallest. The largest skulls are vulture-like, (e.g. no. 50, the Andean condor Vultur gryphus) and the smallest are falconet-like, (e.g. no. 1 Collared falconet Microhierax caerulescens)
No: 49 Tyrannosaurus_James
No: 34 cosmos_germanii
No: 29 gianmarco_linx
No: 27 gerardicus_ridiculus
No: 26 neili_shephardus
No: 25 raoulus
No: 25 mattius_leachia
No: 24 silver bird
No: 21 davidus_wilbyii
No: 21 juan_guerrero
No: 21 hui_wibyli
No: 12 sina_t
No: 7 louisus_alleni
Session Info
sessioninfo::session_info()## - Session info ---------------------------------------------------------------
## setting value
## version R version 4.1.3 (2022-03-10)
## os Windows 10 x64
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United Kingdom.1252
## ctype English_United Kingdom.1252
## tz Europe/London
## date 2022-04-12
##
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## [2] C:/Users/bobturner/AppData/Local/Temp/Rtmpeye7SA/renv-system-library
##
## P -- Loaded and on-disk path mismatch.This projects uses renv
for dependency management.